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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ), 'gf_id' => 'HOM05D001374', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001374' ), 'data_identifier' => 'HOM05D001374', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001374', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21870' => 'bna', 'A02p13900' => 'bna', 'A05p45250' => 'bna', 'A08p26950' => 'bna', 'A08p26960' => 'bna', 'A09p39220' => 'bna', 'A09p55350' => 'bna', 'Aa31LG2G3470' => 'aar', 'Aa31LG2G6960' => 'aar', 'Aa31LG5G13080' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3741' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5697' => 'aag', 'Actinidia01582' => 'ach', 'Actinidia14906' => 'ach', 'Actinidia16665' => 'ach', 'Actinidia17639' => 'ach', 'Actinidia26306' => 'ach', 'Actinidia32419' => 'ach', 'Actinidia36324' => 'ach', 'Ah.02g127600' => 'amhyb', 'Ah.03g138230' => 'amhyb', 'Ah.10g037750' => 'amhyb', 'Ah.16g101750' => 'amhyb', 'AL1G39980' => 'aly', 'AL2G25420' => 'aly', 'AL3G11940' => 'aly', 'AL6G31230' => 'aly', 'AL6G31240' => 'aly', 'Aqoxy3G00262' => 'aox', 'Aqoxy3G00265' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DTRW9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G97L2S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKD07K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YG55AK' => 'arhy', 'AT1G25350' => 'ath', 'AT1G67070' => 'ath', 'AT1G68325' => 'ath', 'AT3G02570' => 'ath', 'AT5G19720' => 'ath', 'ATR0691G154' => 'atr', 'ATR1125G076' => 'atr', 'Atru.chr1.1686' => 'acertr', 'Atru.chr11.139' => 'acertr', 'Atru.chr11.140' => 'acertr', 'Atru.chr11.143' => 'acertr', 'Atru.chr11.144' => 'acertr', 'Atru.chr7.1031' => 'acertr', 'AUR62002537' => 'cqu', 'AUR62002847' => 'cqu', 'AUR62009004' => 'cqu', 'AUR62023298' => 'cqu', 'AUR62023655' => 'cqu', 'AUR62037316' => 'cqu', 'BcaB03g12025' => 'bca', 'BcaB03g12026' => 'bca', 'BcaB03g14037' => 'bca', 'BcaB05g24234' => 'bca', 'BcaB06g26059' => 'bca', 'BcaC01g01691' => 'bca', 'BcaC01g03668' => 'bca', 'BcaC02g12764' => 'bca', 'BcaC03g14793' => 'bca', 'BcaC05g26473' => 'bca', 'BcaC05g26679' => 'bca', 'BcaC05g30366' => 'bca', 'BcaC09g47711' => 'bca', 'BcaNung05404' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00070' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00090' => 'bna', 'BolC1t05894H' => 'bol', 'BolC2t08394H' => 'bol', 'BolC3t17283H' => 'bol', 'BolC3t19594H' => 'bol', 'BolC4t21900H' => 'bol', 'BolC5t31249H' => 'bol', 'BolC5t35076H' => 'bol', 'BolC7t43598H' => 'bol', 'BraA02t06451Z' => 'bra', 'BraA04t17049Z' => 'bra', 'BraA05t19512Z' => 'bra', 'BraA05t23135Z' => 'bra', 'BraA08t34641Z' => 'bra', 'BraA08t34642Z' => 'bra', 'BraA09t39421Z' => 'bra', 'BraSC246t45833Z' => 'bra', 'C01p12810' => 'bna', 'C01p40860' => 'bna', 'C02p22400' => 'bna', 'C03p49890' => 'bna', 'C03p72940' => 'bna', 'C03p83240' => 'bna', 'C04p02560' => 'bna', 'C05p25160' => 'bna', 'C07p30590' => 'bna', 'C09p35310' => 'bna', 'C09p75770' => 'bna', 'CAN.G225.8' => 'can', 'CAN.G225.9' => 'can', 'CAN.G610.65' => 'can', 'CAN.G625.26' => 'can', 'CAN.G82.11' => 'can', 'CAN.G988.6' => 'can', 'CANSAT56G0741' => 'cansat', 'CANSAT78G0747' => 'cansat', 'CARHR026140' => 'chi', 'CARHR059520' => 'chi', 'CARHR061010' => 'chi', 'CARHR061020' => 'chi', 'CARHR061030' => 'chi', 'CARHR076580' => 'chi', 'Carub.0001s2516' => 'cru', 'Carub.0002s1336' => 'cru', 'Carub.0002s1482' => 'cru', 'Carub.0003s0169' => 'cru', 'Carub.0003s3008' => 'cru', 'Ca_04045_v3' => 'car', 'Ca_04052_v3' => 'car', 'Ca_11159_v3' => 'car', 'CBR_g22254' => 'cbr', 'CBR_g3524' => 'cbr', 'Cc07_g08780' => 'ccan', 'Cc11_g09920' => 'ccan', 'CDE02G0451' => 'cde', 'CDE06G1000' => 'cde', 'CDE07G1238' => 'cde', 'CDE07G1626' => 'cde', 'CDE09G0363' => 'cde', 'Cfa007920' => 'cfa', 'Cfa015867' => 'cfa', 'Cfa025355' => 'cfa', 'Ciclev10011731m.g' => 'ccl', 'Ciclev10014320m.g' => 'ccl', 'Ciclev10017881m.g' => 'ccl', 'CiPaw.03G061800' => 'cil', 'CiPaw.05G239400' => 'cil', 'CiPaw.06G018700' => 'cil', 'ClCG01G004780' => 'cla', 'ClCG02G012120' => 'cla', 'ClCG05G011620' => 'cla', 'ClCG11G004350' => 'cla', 'COL.COLO4_06769' => 'col', 'COL.COLO4_07078' => 'col', 'COL.COLO4_09339' => 'col', 'Cpa.g.sc282.4' => 'cpa', 'Cpa.g.sc61.18' => 'cpa', 'Cpa.g.sc798.2' => 'cpa', 'Cre02.g147650' => 'cre', 'Cre14.g614900' => 'cre', 'CsaV3_2G014770' => 'csa', 'CsaV3_2G016280' => 'csa', 'CsaV3_3G020950' => 'csa', 'CsaV3_5G004970' => 'csa', 'CSS0000826' => 'camsi', 'CSS0016974' => 'camsi', 'CSS0028401' => 'camsi', 'CSS0034691' => 'camsi', 'CSS0042454' => 'camsi', 'CSS0047778' => 'camsi', 'DCAR_007251' => 'dca', 'DCAR_017188' => 'dca', 'DCAR_021035' => 'dca', 'DCAR_023602' => 'dca', 'DCAR_023648' => 'dca', 'Dinv09115' => 'din', 'Dinv21062' => 'din', 'Dinv21063' => 'din', 'Dinv31622' => 'din', 'Dinv34820' => 'din', 'Duzib133G0579' => 'dzi', 'Duzib133G1517' => 'dzi', 'Duzib138G1164' => 'dzi', 'Duzib248G1131' => 'dzi', 'Duzib251G0305' => 'dzi', 'ECA232G3200' => 'eca', 'ECA233G2275' => 'eca', 'ECA233G4474' => 'eca', 'ECA233G5383' => 'eca', 'ECA246G4268' => 'eca', 'EL10Ac2g04561' => 'bvu', 'EL10Ac4g08504' => 'bvu', 'EL10Ac6g14344' => 'bvu', 'EL10Ac7g17806' => 'bvu', 'Eucgr.B03004' => 'egr', 'Eucgr.F02498' => 'egr', 'FAN07G0461' => 'fan', 'FAN07G0862' => 'fan', 'FAN08G2237' => 'fan', 'FAN12G2409' => 'fan', 'FAN12G2560' => 'fan', 'FAN12G3668' => 'fan', 'FAN12G3933' => 'fan', 'FAN15G3409' => 'fan', 'FAN17G0272' => 'fan', 'FAN17G1418' => 'fan', 'FAN18G1256' => 'fan', 'FAN20G1553' => 'fan', 'FAN20G1643' => 'fan', 'FAN22G0420' => 'fan', 'FAN22G1012' => 'fan', 'FAN22G1881' => 'fan', 'FAN27G0785' => 'fan', 'FvH4_2g35130' => 'fve', 'FvH4_4g07120' => 'fve', 'FvH4_4g27070' => 'fve', 'FvH4_4g27080' => 'fve', 'FvH4_5g21090' => 'fve', 'Glyma.06G203400' => 'gma', 'Glyma.08G365900' => 'gma', 'Glyma.10G115901' => 'gma', 'Glyma.10G272800' => 'gma', 'Glyma.13G045700' => 'gma', 'Glyma.17G205500' => 'gma', 'Glyma.18G296300' => 'gma', 'Glyma.19G049300' => 'gma', 'Glyma.20G117100' => 'gma', 'Glyma.20G117150' => 'gma', 'Gohir.A05G321600' => 'ghi', 'Gohir.A11G163700' => 'ghi', 'Gohir.A12G053500' => 'ghi', 'Gohir.D05G323900' => 'ghi', 'Gohir.D11G170000' => 'ghi', 'Gohir.D12G052200' => 'ghi', 'Gorai.007G181800' => 'gra', 'Gorai.008G055300' => 'gra', 'Gorai.009G347600' => 'gra', 'GSVIVG01011870001' => 'vvi', 'GSVIVG01011871001' => 'vvi', 'GSVIVG01018308001' => 'vvi', 'GSVIVG01031017001' => 'vvi', 'HanXRQChr08g0213611' => 'han', 'HanXRQChr11g0330631' => 'han', 'HanXRQChr12g0371141' => 'han', 'HanXRQChr12g0375821' => 'han', 'HanXRQChr15g0471471' => 'han', 'HanXRQChr16g0499611' => 'han', 'HanXRQChr16g0508691' => 'han', 'Haze_00619' => 'cav', 'Haze_14157' => 'cav', 'Haze_24085' => 'cav', 'Haze_26608' => 'cav', 'Haze_27216' => 'cav', 'Hma1.2p1_0061F.1_g033680' => 'hma', 'Hma1.2p1_0136F.1_g062290' => 'hma', 'Hma1.2p1_1109F.1_g258040' => 'hma', 'HPP92_021791' => 'vpl', 'HPP92_021863' => 'vpl', 'Hund16159' => 'sun', 'Hund20774' => 'sun', 'Hund30842' => 'sun', 'Hund30844' => 'sun', 'Hund30883' => 'sun', 'Hund30884' => 'sun', 'Lalb_Chr02g0145891' => 'lal', 'Lalb_Chr04g0257481' => 'lal', 'Lalb_Chr06g0166001' => 'lal', 'Lalb_Chr17g0335921' => 'lal', 'Lalb_Chr21g0308841' => 'lal', 'Lj1g0015014' => 'lja', 'Lj2A442T43' => 'lonja', 'Lj2C442T0' => 'lonja', 'Lj4A191T47' => 'lonja', 'Lj4g0028120' => 'lja', 'Lj6C756T1' => 'lonja', 'Lsat_1_v5_gn_2_109180' => 'lsa', 'Lsat_1_v5_gn_2_80001' => 'lsa', 'Lsat_1_v5_gn_3_79700' => 'lsa', 'Lsat_1_v5_gn_4_154001' => 'lsa', 'Lsat_1_v5_gn_6_7841' => 'lsa', 'Lsat_1_v5_gn_8_40760' => 'lsa', 'Manes.01G110800' => 'mes', 'Manes.02G069000' => 'mes', 'Manes.06G066500' => 'mes', 'Manes.14G104300' => 'mes', 'Mapoly0039s0055' => 'mpo', 'Mapoly0082s0088' => 'mpo', 'Mapoly0089s0016' => 'mpo', 'MBI16_g23453_MAGBIO' => 'mbi', 'MBI16_g23455_MAGBIO' => 'mbi', 'MCO01G766' => 'mco', 'MCO03G445' => 'mco', 'MD09G1253100' => 'mdo', 'MD13G1039700' => 'mdo', 'MD13G1039800' => 'mdo', 'MD16G1040600' => 'mdo', 'MD16G1040700' => 'mdo', 'MD17G1244800' => 'mdo', 'Medtr1g110430' => 'mtr', 'Medtr7g007320' => 'mtr', 'MELO3C005458.2' => 'cme', 'MELO3C020220.2' => 'cme', 'MELO3C020839.2' => 'cme', 'MELO3C023301.2' => 'cme', 'MELO3C027179.2' => 'cme', 'Migut.H00220' => 'egut', 'Migut.L00324' => 'egut', 'Migut.L01049' => 'egut', 'Migut.O00776' => 'egut', 'MSTRG.15298' => 'ama', 'MSTRG.2228' => 'ama', 'MSTRG.23577' => 'ama', 'MSTRG.3568' => 'ama', 'MSTRG.850' => 'ama', 'Nitab4.5_0000659g0010' => 'nta', 'Nitab4.5_0000912g0180' => 'nta', 'Nitab4.5_0000965g0090' => 'nta', 'Nitab4.5_0001382g0010' => 'nta', 'Nitab4.5_0001616g0020' => 'nta', 'Nitab4.5_0002207g0040' => 'nta', 'Nitab4.5_0003867g0050' => 'nta', 'Nitab4.5_0005631g0020' => 'nta', 'Nn4g23889' => 'nnu', 'Nn4g23891' => 'nnu', 'Nn5g28146' => 'nnu', 'Oeu008431.1' => 'oeu', 'Oeu030789.1' => 'oeu', 'Oeu039730.1' => 'oeu', 'Oeu039731.1' => 'oeu', 'Oeu054996.3' => 'oeu', 'Oeu059498.1' => 'oeu', 'Os01g0127900' => 'osa', 'Os01g0185200' => 'osa', 'Os05g0182800' => 'osa', 'Os11g0600900' => 'osa', 'Peaxi162Scf00104g00094' => 'pax', 'Peaxi162Scf00394g00617' => 'pax', 'Peaxi162Scf00421g00336' => 'pax', 'Peaxi162Scf00753g00332' => 'pax', 'PGR004G1825' => 'pgr', 'PGR102G0253' => 'pgr', 'PGSC0003DMG400010399' => 'stu', 'PGSC0003DMG400011772' => 'stu', 'PGSC0003DMG400014572' => 'stu', 'PGSC0003DMG400026392' => 'stu', 'Phvul.007G028800' => 'pvu', 'Phvul.008G006200' => 'pvu', 'Potri.004G099100' => 'ptr', 'Potri.008G122200' => 'ptr', 'Potri.010G122866' => 'ptr', 'Potri.010G122932' => 'ptr', 'Potri.017G115500' => 'ptr', 'Pp3c16_5490' => 'ppa', 'Pp3c1_19680' => 'ppa', 'Pp3c6_14770' => 'ppa', 'PRCOL_00001423' => 'pco', 'PRCOL_00001723' => 'pco', 'Prupe.1G313400' => 'ppe', 'Prupe.1G313500' => 'ppe', 'Prupe.3G142100' => 'ppe', 'Psat3g205480' => 'psa', 'Psat5g114400' => 'psa', 'Psat6g226160' => 'psa', 'PSO017G0665' => 'pso', 'PSO063G5256' => 'pso', 'PSO063G7347' => 'pso', 'PSO478G4540' => 'pso', 'PSO782G3382' => 'pso', 'QL01p040852' => 'qlo', 'QL02p051253' => 'qlo', 'QL10p039915' => 'qlo', 'RcHm_v2.0_Chr1g0324521' => 'rch', 'RcHm_v2.0_Chr1g0324531' => 'rch', 'RcHm_v2.0_Chr1g0324551' => 'rch', 'RcHm_v2.0_Chr1g0324791' => 'rch', 'RcHm_v2.0_Chr1g0324801' => 'rch', 'RcHm_v2.0_Chr4g0399291' => 'rch', 'RcHm_v2.0_Chr4g0434871' => 'rch', 'RcHm_v2.0_Chr4g0434881' => 'rch', 'RcHm_v2.0_Chr5g0081291' => 'rch', 'RcHm_v2.0_Chr6g0267171' => 'rch', 'RcHm_v2.0_Chr6g0267551' => 'rch', 'RcHm_v2.0_Chr6g0267561' => 'rch', 'RcHm_v2.0_Chr6g0267571' => 'rch', 'RcHm_v2.0_Chr6g0306831' => 'rch', 'RcHm_v2.0_Chr7g0208121' => 'rch', 'RcHm_v2.0_Chr7g0208231' => 'rch', 'Rhsim08G0082500' => 'rsi', 'Rhsim09G0106300' => 'rsi', 'Rhsim10G0067600' => 'rsi', 'Sabra04G0080800' => 'sbr', 'Sabra08G0092800' => 'sbr', 'Sabra10G0093000' => 'sbr', 'Sabra17G0095700' => 'sbr', 'SalBow3G2503' => 'sbo', 'SalBow5G2511' => 'sbo', 'SalBow8G3975' => 'sbo', 'SalBow8G5161' => 'sbo', 'Sc10g0001150' => 'sci', 'Sc14g0007390' => 'sci', 'Sed0001283' => 'sed', 'Sed0010965' => 'sed', 'Sed0014729' => 'sed', 'Sed0017350' => 'sed', 'Sed0019956' => 'sed', 'SEGI_13900' => 'sgi', 'SEGI_18350' => 'sgi', 'SEGI_36555' => 'sgi', 'SGA_v2.0_scaffold32G13114' => 'sas', 'SGA_v2.0_scaffold38G14957' => 'sas', 'SGA_v2.0_scaffold49G18110' => 'sas', 'SHI32754' => 'shi', 'SMO339G0074' => 'smo', 'SMO347G0322' => 'smo', 'SMO361G0577' => 'smo', 'SMO361G0624' => 'smo', 'Solyc02g063220.3' => 'sly', 'Solyc02g086090.4' => 'sly', 'Solyc05g009220.3' => 'sly', 'Solyc06g060100.3' => 'sly', 'Sopen02g014290' => 'spe', 'Sopen02g030780' => 'spe', 'Sopen05g004940' => 'spe', 'Sopen06g020210' => 'spe', 'Sp1g22870' => 'spa', 'Sp3g01610' => 'spa', 'Sp5g22000' => 'spa', 'TAR140G0001' => 'tar', 'TAR362G0805' => 'tar', 'TAR371G0094' => 'tar', 'TAR371G0613' => 'tar', 'TAR371G0884' => 'tar', 'TAR371G0932' => 'tar', 'TAR374G1395' => 'tar', 'TAR623G0829' => 'tar', 'TAR629G2539' => 'tar', 'THA.LOC104805568' => 'tha', 'THA.LOC104808353' => 'tha', 'THA.LOC104820945' => 'tha', 'THA.LOC104821915' => 'tha', 'Thecc.04G133200' => 'tca', 'Thecc.07G144700' => 'tca', 'Thhalv10006840m.g' => 'esa', 'Thhalv10018552m.g' => 'esa', 'Thhalv10020776m.g' => 'esa', 'TPR.G4913' => 'tpr', 'TPR.G9701' => 'tpr', 'TWI74G1455' => 'twi', 'TWI77G0977' => 'twi', 'TWI79G1774' => 'twi', 'unitig_22.g5575' => 'ugi', 'unitig_24.g30583' => 'ugi', 'unitig_8.g3596' => 'ugi', 'vmacro05551' => 'vma', 'vmacro10571' => 'vma', 'vmacro18074' => 'vma', 'VMungo0331G1845' => 'vmu', 'VMungo0720G1962' => 'vmu', 'VMungo1383G1329' => 'vmu', 'Zm00001eb121810' => 'zma', 'Zm00001eb125530' => 'zma', 'Zm00001eb167360' => 'zma', 'Zm00001eb230120' => 'zma', 'Zm00001eb266540' => 'zma', 'Zm00001eb335020' => 'zma', 'Zm00001eb335030' => 'zma', 'Zm00001eb337800' => 'zma' ) $gf_id = 'HOM05D001374' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001374' ) $data_identifier = 'HOM05D001374' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 2, 'lonja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 16, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb337800' $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